Autotune PID values not used in FBWA and other modes

On my Wing Wing z84 I use an APM 2.8 with Arduplane 3.4. I know this is archaic hardware and software. But I have it laying around so why not use it.

I have performed an extended autotune flight and I am pretty happy with the results. As far as I know the PID values are storen every ten seconds. I can confirm that every time I fly in autotune it behaves according to these new PID values. That's great. It also seems that these PID values are persistent accross shutdowns of the APM. That's also great.

The issue is that in any of the other assisted modes like FBWA, FBWB, Loiter, etc the old wrong PID values are used causing major oscillations and it will crash with these PID's.

In Mission Planner I can indeed see the wrong PID's at the Basic Tuning page.

My question is simple: Why are the PID's acquired in autotune not used in any other flight mode? It looks like I am forced to do a manual tune. That is something I don't want because autotune works quite nice.